FLC OF A MD88 OVERSHOT DSCNT ALT DUE TO MISPROGRAMMING THE AUTOPLT ALT CAPTURE MODE. THEY RECOGNIZED THEIR MISTAKE AND DISCONNECTED THE AUTOPLT AND RETURNED TO ASSIGNED ALT.

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DURING ENRTE DSCNT PASSING THROUGH FL255 WITH CLRNC TO FL240; ZNY CLRED US TO CONTINUE DSCNT TO FL220 AND TO SLOW FROM 330 KIAS TO 250 KIAS. PASSING FL233; CTR REVISED CLRNC AND TOLD US TO MAINTAIN FL230. I (PNF) GAVE THE READBACK; THEN PLACED 230 IN THE AUTOPLT ALT CAPTURE WINDOW. AT THE SAME TIME VERBALIZING TO THE CAPT TO LEVEL OFF AT FL230. DURING THE REVISED CLRNC UNTIL NOW THE CAPT WAS ADJUSTING THE ACFT'S SPD IN IAS PITCH MODE AND DIDN'T REALIZE WE WERE LESS THAN 300 FT FROM REVISED LEVELOFF; WITH A DSCNT RATE OF APPROX 1500 FPM. SINCE I HAD PLACED FL230 IN THE ALT CAPTURE WINDOW; I WAS EXPECTING AN IMMEDIATE ALT CAPTURE BY THE AUTOPLT. THAT DID NOT HAPPEN BECAUSE THE CAPT WAS MOVING THE IAS-VERT SPD THUMB WHEEL AND WE WERE NOW IN VERT SPD. AT FL230 I AGAIN STATED 'LEVEL OFF AT FL230; STOP HERE' AND PUSHED THE ALT HOLD BUTTON ON THE AUTOPLT. SINCE THE CAPT WAS STILL WORKING THE THUMB WHEEL THE ALT CAPTURE WAS LOST. PASSING APPROX FL228 THE CAPT REALIZED WE WERE DSNDING THROUGH FL230 AND DISCONNECTED THE AUTOPLT AND RETURNED THE ACFT TO FL230. WE STOPPED OUR DSCNT APPROX 400 FT LOW.